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Merge pull request #384 from ssjunnebo/572251_reduce_min_gene_size
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Reduce min gene size
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@andrewjpage
andrewjpage authored Jan 23, 2018
2 parents 0cc158c + ae7ac49 commit 0b69516
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Showing 11 changed files with 21 additions and 21 deletions.
2 changes: 1 addition & 1 deletion dist.ini
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Expand Up @@ -3,7 +3,7 @@ author = Andrew J. Page <[email protected]>
license = GPL_3
copyright_holder = Wellcome Trust Sanger Institute
copyright_year = 2013
version = 3.11.4
version = 3.12.0
main_module = lib/Bio/Roary.pm

[MetaResources]
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2 changes: 1 addition & 1 deletion lib/Bio/Roary/BedFromGFFRole.pm
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Expand Up @@ -13,7 +13,7 @@ use Moose::Role;
use Bio::Tools::GFF;

has '_tags_to_filter' => ( is => 'ro', isa => 'Str', default => '(CDS|ncRNA|tRNA|tmRNA|rRNA)' );
has 'min_gene_size_in_nucleotides' => ( is => 'ro', isa => 'Int', default => 120 );
has 'min_gene_size_in_nucleotides' => ( is => 'ro', isa => 'Int', default => 18 );
has 'output_directory' => ( is => 'ro', isa => 'Str', default => '.' );

sub _bed_output_filename {
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2 changes: 1 addition & 1 deletion t/data/example_annotation.gff
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Expand Up @@ -12,7 +12,7 @@ abc|SC|contig000001 RNAmmer:1.2 rRNA 7556 9112 . + 0 ID=abc_01705;inference=COOR
abc|SC|contig000001 Prodigal:2.60 CDS 9419 9646 . + 0 ID=abc_00010;inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00010;product=hypothetical protein;protein_id=gnl|SC|abc_00010
abc|SC|contig000001 Prodigal:2.60 CDS 9952 10899 . - 0 ID=abc_00011;inference=ab initio prediction:Prodigal:2.60,protein motif:Pfam:PF03595.11;locus_tag=abc_00011;product=C4-dicarboxylate transporter/malic acid transport protein;protein_id=gnl|SC|abc_00011
abc|SC|contig000001 Prodigal:2.60 CDS 11148 11336 . + 0 ID=abc_00012;inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00012;product=hypothetical protein;protein_id=gnl|SC|abc_00012
abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11878 . - 0 ID=abc_00013;inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct)
abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11820 . - 0 ID=abc_00013;inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct)
abc|SC|contig000001 Prodigal:2.60 CDS 12241 12375 . + 0 ID=abc_00014;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00014;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00014
abc|SC|contig000001 Prodigal:2.60 CDS 12432 12566 . + 0 ID=abc_00015;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00015;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00015
abc|SC|contig000001 Prodigal:2.60 CDS 12699 13385 . + 0 ID=abc_00016;eC_number=3.-.-.-;gene=yfnB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:O06480,protein motif:CLUSTERS:PRK09449,protein motif:TIGRFAMs:TIGR02254,protein motif:Pfam:PF00702.1;locus_tag=abc_00016;product=Putative HAD-hydrolase yfnB,dUMP phosphatase,HAD hydrolase,haloacid dehalogenase-like hydrolase;protein_id=gnl|SC|abc_00016
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2 changes: 1 addition & 1 deletion t/data/example_annotation_2.gff
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Expand Up @@ -12,7 +12,7 @@ abc|SC|contig000001 RNAmmer:1.2 rRNA 7556 9112 . + 0 ID=abc_01705;inference=COOR
abc|SC|contig000001 Prodigal:2.60 CDS 9419 9646 . + 0 ID=abc_00010;inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00010;product=hypothetical protein;protein_id=gnl|SC|abc_00010
abc|SC|contig000001 Prodigal:2.60 CDS 9952 10899 . - 0 ID=abc_00011;inference=ab initio prediction:Prodigal:2.60,protein motif:Pfam:PF03595.11;locus_tag=abc_00011;product=C4-dicarboxylate transporter/malic acid transport protein;protein_id=gnl|SC|abc_00011
abc|SC|contig000001 Prodigal:2.60 CDS 11148 11336 . + 0 ID=abc_00012;inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00012;product=hypothetical protein;protein_id=gnl|SC|abc_00012
abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11878 . - 0 ID=abc_00013;inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct)
abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11820 . - 0 ID=abc_00013;inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct)
abc|SC|contig000001 Prodigal:2.60 CDS 12241 12375 . + 0 ID=abc_00014;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00014;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00014
abc|SC|contig000001 Prodigal:2.60 CDS 12432 12566 . + 0 ID=abc_00015;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00015;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00015
abc|SC|contig000001 Prodigal:2.60 CDS 12699 13385 . + 0 ID=abc_00016;eC_number=3.-.-.-;gene=yfnB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:O06480,protein motif:CLUSTERS:PRK09449,protein motif:TIGRFAMs:TIGR02254,protein motif:Pfam:PF00702.1;locus_tag=abc_00016;product=Putative HAD-hydrolase yfnB,dUMP phosphatase,HAD hydrolase,haloacid dehalogenase-like hydrolase;protein_id=gnl|SC|abc_00016
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6 changes: 3 additions & 3 deletions t/data/genbank_gbff/genbank2.gff
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Expand Up @@ -17,9 +17,9 @@ CVBR01000001 GenBank gene 4176 6542 . + 1 ID=ERS325340_00004;Name=sspH2;locus_ta
CVBR01000001 GenBank mRNA 4176 6542 . + 1 ID=ERS325340_00004.t01;Parent=ERS325340_00004
CVBR01000001 GenBank CDS 4176 6542 . + 1 ID=ERS325340_00004.p01;Parent=ERS325340_00004.t01;Dbxref=GI:804333229;eC_number=6.3.2.-;Name=sspH2;codon_start=1;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002244314.1;locus_tag=ERS325340_00004;product=secreted effector protein;protein_id=CQU31395.1;transl_table=11;translation=length.788
CVBR01000001 GenBank exon 4176 6542 . + 1 Parent=ERS325340_00004.t01
CVBR01000001 GenBank gene 7163 7239 . - 1 ID=ERS325340_00005;Name=ERS325340_00005
CVBR01000001 GenBank tRNA 7163 7239 . - 1 ID=ERS325340_00005.r01;Parent=ERS325340_00005;Name=ERS325340_00005;inference=COORDINATES: profile:Aragorn:1.2.36;product=tRNA-Pro
CVBR01000001 GenBank exon 7163 7239 . - 1 Parent=ERS325340_00005.r01;Name=ERS325340_00005
CVBR01000001 GenBank gene 7163 7180 . - 1 ID=ERS325340_00005;Name=ERS325340_00005
CVBR01000001 GenBank tRNA 7163 7180 . - 1 ID=ERS325340_00005.r01;Parent=ERS325340_00005;Name=ERS325340_00005;inference=COORDINATES: profile:Aragorn:1.2.36;product=tRNA-Pro
CVBR01000001 GenBank exon 7163 7180 . - 1 Parent=ERS325340_00005.r01;Name=ERS325340_00005
##FASTA
>CVBR01000001
TAGAGCGCAGTATCCGGCTGGCGCAGGAGAAATAAGACCCTGACGGCCCGGTGGCGTGGC
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6 changes: 3 additions & 3 deletions t/data/genbank_gbff/genbank3.gff
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Expand Up @@ -17,9 +17,9 @@ CVBT01000001 GenBank gene 4180 6546 . + 1 ID=ERS325326_00004;Name=sspH2;locus_ta
CVBT01000001 GenBank mRNA 4180 6546 . + 1 ID=ERS325326_00004.t01;Parent=ERS325326_00004
CVBT01000001 GenBank CDS 4180 6546 . + 1 ID=ERS325326_00004.p01;Parent=ERS325326_00004.t01;Dbxref=GI:804342842;eC_number=6.3.2.-;Name=sspH2;codon_start=1;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002244314.1;locus_tag=ERS325326_00004;product=secreted effector protein;protein_id=CQU32561.1;transl_table=11;translation=length.788
CVBT01000001 GenBank exon 4180 6546 . + 1 Parent=ERS325326_00004.t01
CVBT01000001 GenBank gene 7167 7243 . - 1 ID=ERS325326_00005;Name=ERS325326_00005
CVBT01000001 GenBank tRNA 7167 7243 . - 1 ID=ERS325326_00005.r01;Parent=ERS325326_00005;Name=ERS325326_00005;inference=COORDINATES: profile:Aragorn:1.2.36;product=tRNA-Pro
CVBT01000001 GenBank exon 7167 7243 . - 1 Parent=ERS325326_00005.r01;Name=ERS325326_00005
CVBT01000001 GenBank gene 7167 7184 . - 1 ID=ERS325326_00005;Name=ERS325326_00005
CVBT01000001 GenBank tRNA 7167 7184 . - 1 ID=ERS325326_00005.r01;Parent=ERS325326_00005;Name=ERS325326_00005;inference=COORDINATES: profile:Aragorn:1.2.36;product=tRNA-Pro
CVBT01000001 GenBank exon 7167 7184 . - 1 Parent=ERS325326_00005.r01;Name=ERS325326_00005
##FASTA
>CVBT01000001
GTGATAGAGCGCAGTATCCGGCTGGCGCAGGAGAAATAAGACCCTGACGGCCCGGTGGCG
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2 changes: 1 addition & 1 deletion t/data/locus_tag_gffs/query_1.gff
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Expand Up @@ -12,7 +12,7 @@ abc|SC|contig000001 RNAmmer:1.2 rRNA 7556 9112 . + 0 inference=COORDINATES:profi
abc|SC|contig000001 Prodigal:2.60 CDS 9419 9646 . + 0 inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00010;product=hypothetical protein;protein_id=gnl|SC|abc_00010
abc|SC|contig000001 Prodigal:2.60 CDS 9952 10899 . - 0 inference=ab initio prediction:Prodigal:2.60,protein motif:Pfam:PF03595.11;locus_tag=abc_00011;product=C4-dicarboxylate transporter/malic acid transport protein;protein_id=gnl|SC|abc_00011
abc|SC|contig000001 Prodigal:2.60 CDS 11148 11336 . + 0 inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00012;product=hypothetical protein;protein_id=gnl|SC|abc_00012
abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11878 . - 0 inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct)
abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11820 . - 0 inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct)
abc|SC|contig000001 Prodigal:2.60 CDS 12241 12375 . + 0 inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00014;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00014
abc|SC|contig000001 Prodigal:2.60 CDS 12432 12566 . + 0 inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00015;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00015
abc|SC|contig000001 Prodigal:2.60 CDS 12699 13385 . + 0 eC_number=3.-.-.-;gene=yfnB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:O06480,protein motif:CLUSTERS:PRK09449,protein motif:TIGRFAMs:TIGR02254,protein motif:Pfam:PF00702.1;locus_tag=abc_00016;product=Putative HAD-hydrolase yfnB,dUMP phosphatase,HAD hydrolase,haloacid dehalogenase-like hydrolase;protein_id=gnl|SC|abc_00016
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2 changes: 1 addition & 1 deletion t/data/locus_tag_gffs/query_2.gff
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Expand Up @@ -12,7 +12,7 @@ abc|SC|contig000001 RNAmmer:1.2 rRNA 7556 9112 . + 0 inference=COORDINATES:profi
abc|SC|contig000001 Prodigal:2.60 CDS 9419 9646 . + 0 inference=ab initio prediction:Prodigal:2.60;locus_tag="zzz_00010";product=hypothetical protein;protein_id=gnl|SC|abc_00010
abc|SC|contig000001 Prodigal:2.60 CDS 9952 10899 . - 0 inference=ab initio prediction:Prodigal:2.60,protein motif:Pfam:PF03595.11;locus_tag="zzz_00011";product=C4-dicarboxylate transporter/malic acid transport protein;protein_id=gnl|SC|abc_00011
abc|SC|contig000001 Prodigal:2.60 CDS 11148 11336 . + 0 inference=ab initio prediction:Prodigal:2.60;locus_tag="zzz_00012";product=hypothetical protein;protein_id=gnl|SC|abc_00012
abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11878 . - 0 inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag="zzz_00013";product=tRNA-Arg(tct)
abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11820 . - 0 inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag="zzz_00013";product=tRNA-Arg(tct)
abc|SC|contig000001 Prodigal:2.60 CDS 12241 12375 . + 0 inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag="zzz_00014";product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00014
abc|SC|contig000001 Prodigal:2.60 CDS 12432 12566 . + 0 inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag="zzz_00015";product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00015
abc|SC|contig000001 Prodigal:2.60 CDS 12699 13385 . + 0 eC_number=3.-.-.-;gene=yfnB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:O06480,protein motif:CLUSTERS:PRK09449,protein motif:TIGRFAMs:TIGR02254,protein motif:Pfam:PF00702.1;locus_tag="zzz_00016";product=Putative HAD-hydrolase yfnB,dUMP phosphatase,HAD hydrolase,haloacid dehalogenase-like hydrolase;protein_id=gnl|SC|abc_00016
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2 changes: 1 addition & 1 deletion t/data/locus_tag_gffs/query_3.gff
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Expand Up @@ -12,7 +12,7 @@ abc|SC|contig000001 RNAmmer:1.2 rRNA 7556 9112 . + 0 inference=COORDINATES:profi
abc|SC|contig000001 Prodigal:2.60 CDS 9419 9646 . + 0 inference=ab initio prediction:Prodigal:2.60;locus_tag=xxx_00010;product=hypothetical protein;protein_id=gnl|SC|abc_00010
abc|SC|contig000001 Prodigal:2.60 CDS 9952 10899 . - 0 inference=ab initio prediction:Prodigal:2.60,protein motif:Pfam:PF03595.11;locus_tag=xxx_00011;product=C4-dicarboxylate transporter/malic acid transport protein;protein_id=gnl|SC|abc_00011
abc|SC|contig000001 Prodigal:2.60 CDS 11148 11336 . + 0 inference=ab initio prediction:Prodigal:2.60;locus_tag=xxx_00012;product=hypothetical protein;protein_id=gnl|SC|abc_00012
abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11878 . - 0 inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=xxx_00013;product=tRNA-Arg(tct)
abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11820 . - 0 inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=xxx_00013;product=tRNA-Arg(tct)
abc|SC|contig000001 Prodigal:2.60 CDS 12241 12375 . + 0 inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=xxx_00014;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00014
abc|SC|contig000001 Prodigal:2.60 CDS 12432 12566 . + 0 inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=xxx_00015;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00015
abc|SC|contig000001 Prodigal:2.60 CDS 12699 13385 . + 0 eC_number=3.-.-.-;gene=yfnB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:O06480,protein motif:CLUSTERS:PRK09449,protein motif:TIGRFAMs:TIGR02254,protein motif:Pfam:PF00702.1;locus_tag=xxx_00016;product=Putative HAD-hydrolase yfnB,dUMP phosphatase,HAD hydrolase,haloacid dehalogenase-like hydrolase;protein_id=gnl|SC|abc_00016
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